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<h1 class="epydoc">Source Code for <a href="trunk.BIP.Bayes.like-module.html">Module trunk.BIP.Bayes.like</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment"># -*- coding:utf-8 -*-</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment">#-----------------------------------------------------------------------------</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-comment"># Name:        like.py</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-comment"># Project:  BayesianInference</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-comment"># Purpose:     log-likelihood functions</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-comment"># Author:      Fl&#225;vio Code&#231;o Coelho &lt;fccoelho@gmail.com&gt;</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-comment"># Created:     2008-11-26</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-comment"># Copyright:   (c) 2008 by the Author</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-comment"># Licence:     GPL v3</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-comment">#-----------------------------------------------------------------------------</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-name">__docformat__</tt> <tt class="py-op">=</tt> <tt class="py-docstring">"restructuredtext en"</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">random</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">scipy</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">special</tt> <tt class="py-keyword">import</tt> <tt class="py-name">gammaln</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">array</tt><tt class="py-op">,</tt> <tt class="py-name">searchsorted</tt><tt class="py-op">,</tt><tt class="py-name">log</tt><tt class="py-op">,</tt> <tt class="py-name">random</tt><tt class="py-op">,</tt><tt class="py-name">pi</tt><tt class="py-op">,</tt><tt class="py-name">sum</tt><tt class="py-op">,</tt> <tt class="py-name">inf</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"> </tt>
<a name="Categor"></a><div id="Categor-def"><a name="L20"></a><tt class="py-lineno"> 20</tt> <a class="py-toggle" href="#" id="Categor-toggle" onclick="return toggle('Categor');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.like-module.html#Categor">Categor</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt><tt class="py-param">hist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Categor-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Categor-expanded"><a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-docstring">    Categorical Log-likelihood</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-docstring">    generalization of a Bernoulli process for variables with any constant</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-docstring">    number of discrete values.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-docstring">    :Parameters:</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-docstring">        - `x`: data vector (list)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"><tt class="py-docstring">        - `hist`: tuple (prob,classes) classes contain the superior limit of the histogram classes</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; Categor([1],([.3,.7],[0,1]))</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-docstring">    -0.356674943939</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">    <tt id="link-0" class="py-name" targets="Module trunk.BIP.Bayes.like=trunk.BIP.Bayes.like-module.html"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-0', 'like', 'link-0');">like</a></tt> <tt class="py-op">=</tt><tt class="py-number">0.0</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">    <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">    <tt class="py-name">prob</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">hist</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">    <tt class="py-name">sup</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">hist</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">    <tt class="py-name">ind</tt> <tt class="py-op">=</tt> <tt class="py-name">searchsorted</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">    <tt id="link-1" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-1', 'like', 'link-0');">like</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">prob</tt><tt class="py-op">[</tt><tt class="py-name">ind</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-2" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-2', 'like', 'link-0');">like</a></tt> </tt>
</div><a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"> </tt>
<a name="Uniform"></a><div id="Uniform-def"><a name="L41"></a><tt class="py-lineno"> 41</tt> <a class="py-toggle" href="#" id="Uniform-toggle" onclick="return toggle('Uniform');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.like-module.html#Uniform">Uniform</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt><tt class="py-param">min</tt><tt class="py-op">,</tt><tt class="py-param">max</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Uniform-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Uniform-expanded"><a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"><tt class="py-docstring">    Uniform Log-likelihood</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-docstring">    :Parameters:</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-docstring">        - `x`: data vector(list)</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-docstring">        - `min`: lower limit of the distribution</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-docstring">        - `max`: upper limit of the distribution</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; Uniform([1.1,2.3,3.4,4],0,5)</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"><tt class="py-docstring">    -6.4377516497364011</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">max</tt><tt class="py-op">&gt;</tt><tt class="py-name">min</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">    <tt id="link-3" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-3', 'like', 'link-0');">like</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">    <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">max</tt><tt class="py-op">-</tt><tt class="py-name">min</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">&gt;</tt><tt class="py-name">min</tt> <tt class="py-keyword">and</tt> <tt class="py-name">i</tt><tt class="py-op">&lt;=</tt><tt class="py-name">max</tt><tt class="py-op">:</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">            <tt id="link-4" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-4', 'like', 'link-0');">like</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">            <tt id="link-5" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-5', 'like', 'link-0');">like</a></tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-name">inf</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt id="link-6" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-6', 'like', 'link-0');">like</a></tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-7" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-7', 'like', 'link-0');">like</a></tt> </tt>
</div><a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"> </tt>
<a name="Normal"></a><div id="Normal-def"><a name="L64"></a><tt class="py-lineno"> 64</tt> <a class="py-toggle" href="#" id="Normal-toggle" onclick="return toggle('Normal');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.like-module.html#Normal">Normal</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt><tt class="py-param">mu</tt><tt class="py-op">,</tt><tt class="py-param">tau</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Normal-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Normal-expanded"><a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line"><tt class="py-docstring">    Normal Log-like </tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"><tt class="py-docstring">    :Parameters:</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"><tt class="py-docstring">        -  `mu`: mean</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"><tt class="py-docstring">        -  `tau`: precision (1/variance)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; Normal([0],0,1)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt class="py-docstring">    -0.918938533205</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">    <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">    <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">size</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">    <tt id="link-8" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-8', 'like', 'link-0');">like</a></tt> <tt class="py-op">=</tt>  <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt> <tt class="py-op">*</tt> <tt class="py-name">tau</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">-</tt><tt class="py-name">mu</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">    <tt id="link-9" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-9', 'like', 'link-0');">like</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">n</tt><tt class="py-op">*</tt><tt class="py-number">0.5</tt><tt class="py-op">*</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-number">0.5</tt><tt class="py-op">*</tt><tt class="py-name">tau</tt><tt class="py-op">/</tt><tt class="py-name">pi</tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-10" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-10', 'like', 'link-0');">like</a></tt> </tt>
</div><a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"> </tt>
<a name="find_best_tau"></a><div id="find_best_tau-def"><a name="L81"></a><tt class="py-lineno"> 81</tt> <a class="py-toggle" href="#" id="find_best_tau-toggle" onclick="return toggle('find_best_tau');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.like-module.html#find_best_tau">find_best_tau</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt><tt class="py-param">mu</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="find_best_tau-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="find_best_tau-expanded"><a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line"><tt class="py-docstring">    returns the value of tau which maximizes normal loglik for a fixed (x,mu)</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">mu</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">        <tt class="py-name">tau</tt> <tt class="py-op">=</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">mu</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">        <tt class="py-name">tau</tt><tt class="py-op">=</tt><tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">mu</tt> <tt class="py-comment">#starting point</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">    <tt class="py-name">ll</tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name" targets="Function trunk.BIP.Bayes.like.Normal()=trunk.BIP.Bayes.like-module.html#Normal"><a title="trunk.BIP.Bayes.like.Normal" class="py-name" href="#" onclick="return doclink('link-11', 'Normal', 'link-11');">Normal</a></tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">mu</tt><tt class="py-op">,</tt><tt class="py-name">tau</tt><tt class="py-op">)</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">    <tt class="py-name">i</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">;</tt><tt class="py-name">j</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">    <tt class="py-keyword">while</tt> <tt class="py-name">i</tt> <tt class="py-op">&lt;</tt> <tt class="py-number">1000</tt> <tt class="py-keyword">and</tt> <tt class="py-name">j</tt><tt class="py-op">&lt;</tt><tt class="py-number">100000</tt><tt class="py-op">:</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">        <tt class="py-name">taun</tt> <tt class="py-op">=</tt> <tt class="py-name">tau</tt> <tt class="py-op">+</tt> <tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">normal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">        <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="trunk.BIP.Bayes.like.Normal" class="py-name" href="#" onclick="return doclink('link-12', 'Normal', 'link-11');">Normal</a></tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">mu</tt><tt class="py-op">,</tt><tt class="py-name">taun</tt><tt class="py-op">)</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">l</tt><tt class="py-op">&gt;</tt><tt class="py-name">ll</tt><tt class="py-op">:</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">            <tt class="py-name">tau</tt> <tt class="py-op">=</tt> <tt class="py-name">taun</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">            <tt class="py-name">ll</tt> <tt class="py-op">=</tt> <tt class="py-name">l</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">            <tt class="py-name">i</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">        <tt class="py-name">j</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">tau</tt> </tt>
</div><a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line"> </tt>
<a name="Lognormal"></a><div id="Lognormal-def"><a name="L101"></a><tt class="py-lineno">101</tt> <a class="py-toggle" href="#" id="Lognormal-toggle" onclick="return toggle('Lognormal');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.like-module.html#Lognormal">Lognormal</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt><tt class="py-param">mu</tt><tt class="py-op">,</tt><tt class="py-param">tau</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Lognormal-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Lognormal-expanded"><a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line"><tt class="py-docstring">    Lognormal Log-likelihood</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line"><tt class="py-docstring">    :Parameters:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line"><tt class="py-docstring">        -  `mu`: mean</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line"><tt class="py-docstring">        -  `tau`: precision (1/sd)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; Lognormal([0.5,1,1.2],0,0.5)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line"><tt class="py-docstring">    -3.15728720569</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">    <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">    <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">size</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">    <tt id="link-13" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-13', 'like', 'link-0');">like</a></tt> <tt class="py-op">=</tt> <tt class="py-name">n</tt> <tt class="py-op">*</tt> <tt class="py-number">0.5</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">tau</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-number">2.0</tt><tt class="py-op">*</tt><tt class="py-name">pi</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-number">0.5</tt><tt class="py-op">*</tt><tt class="py-name">tau</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">mu</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> <tt class="py-op">-</tt> <tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-op">-</tt><tt id="link-14" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-14', 'like', 'link-0');">like</a></tt> </tt>
</div><a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line"> </tt>
<a name="Poisson"></a><div id="Poisson-def"><a name="L117"></a><tt class="py-lineno">117</tt> <a class="py-toggle" href="#" id="Poisson-toggle" onclick="return toggle('Poisson');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.like-module.html#Poisson">Poisson</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt><tt class="py-param">mu</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Poisson-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Poisson-expanded"><a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line"><tt class="py-docstring">    Poisson Log-Likelihood function </tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; Poisson([2],2)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line"><tt class="py-docstring">    -1.30685281944</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">    <tt class="py-name">x</tt><tt class="py-op">=</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">    <tt class="py-name">sumx</tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">*</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">mu</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">mu</tt><tt class="py-op">)</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">    <tt class="py-name">sumfact</tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">factorial</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">    <tt id="link-15" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-15', 'like', 'link-0');">like</a></tt> <tt class="py-op">=</tt> <tt class="py-name">sumx</tt><tt class="py-op">-</tt><tt class="py-name">sumfact</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-16" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-16', 'like', 'link-0');">like</a></tt> </tt>
</div><a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line"> </tt>
<a name="Negbin"></a><div id="Negbin-def"><a name="L129"></a><tt class="py-lineno">129</tt> <a class="py-toggle" href="#" id="Negbin-toggle" onclick="return toggle('Negbin');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.like-module.html#Negbin">Negbin</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt><tt class="py-param">r</tt><tt class="py-op">,</tt><tt class="py-param">p</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Negbin-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Negbin-expanded"><a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line"><tt class="py-docstring">    Negative Binomial Log-Likelihood </tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; Negbin([2,3],6,0.3)</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line"><tt class="py-docstring">    -9.16117424315</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line">    <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">    <tt id="link-17" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-17', 'like', 'link-0');">like</a></tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt id="link-18" class="py-name" targets="Variable trunk.BIP.SDE.example.r=trunk.BIP.SDE.example-module.html#r"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-18', 'r', 'link-18');">r</a></tt><tt class="py-op">*</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">x</tt><tt class="py-op">*</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">p</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">factorial</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">+</tt><tt id="link-19" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-19', 'r', 'link-18');">r</a></tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">factorial</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">factorial</tt><tt class="py-op">(</tt><tt id="link-20" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-20', 'r', 'link-18');">r</a></tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-21" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-21', 'like', 'link-0');">like</a></tt> </tt>
</div><a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line"> </tt>
<a name="Binomial"></a><div id="Binomial-def"><a name="L139"></a><tt class="py-lineno">139</tt> <a class="py-toggle" href="#" id="Binomial-toggle" onclick="return toggle('Binomial');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.like-module.html#Binomial">Binomial</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt><tt class="py-param">n</tt><tt class="py-op">,</tt><tt class="py-param">p</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Binomial-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Binomial-expanded"><a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line"><tt class="py-docstring">    Binomial Log-Likelihood </tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; Binomial([2,3],6,0.3)</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line"><tt class="py-docstring">    -2.81280615454</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">    <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">    <tt id="link-22" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-22', 'like', 'link-0');">like</a></tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">*</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">)</tt><tt class="py-op">+</tt> <tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">-</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-number">1.</tt><tt class="py-op">-</tt><tt class="py-name">p</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">factorial</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">factorial</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">factorial</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">-</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-23" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-23', 'like', 'link-0');">like</a></tt> </tt>
</div><a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line"> </tt>
<a name="Weibull"></a><div id="Weibull-def"><a name="L149"></a><tt class="py-lineno">149</tt> <a class="py-toggle" href="#" id="Weibull-toggle" onclick="return toggle('Weibull');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.like-module.html#Weibull">Weibull</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt><tt class="py-param">alpha</tt><tt class="py-op">,</tt><tt class="py-param">beta</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Weibull-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Weibull-expanded"><a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line"><tt class="py-docstring">    Log-Like Weibull</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; Weibull([2,1,0.3,.5,1.7],1.5,3)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line"><tt class="py-docstring">    -7.811955373</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">    <tt class="py-name">x</tt><tt class="py-op">=</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">    <tt class="py-name">beta</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">beta</tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">    <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">size</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">    <tt class="py-comment">#Normalizing constant</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">    <tt id="link-24" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-24', 'like', 'link-0');">like</a></tt> <tt class="py-op">=</tt> <tt class="py-name">n</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">alpha</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-name">alpha</tt><tt class="py-op">*</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">beta</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">    <tt class="py-comment"># Kernel of the distribution</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">    <tt id="link-25" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-25', 'like', 'link-0');">like</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">alpha</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">/</tt><tt class="py-name">beta</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-name">alpha</tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-26" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-26', 'like', 'link-0');">like</a></tt> </tt>
</div><a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line"> </tt>
<a name="Bernoulli"></a><div id="Bernoulli-def"><a name="L164"></a><tt class="py-lineno">164</tt> <a class="py-toggle" href="#" id="Bernoulli-toggle" onclick="return toggle('Bernoulli');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.like-module.html#Bernoulli">Bernoulli</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt><tt class="py-param">p</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Bernoulli-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Bernoulli-expanded"><a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line"><tt class="py-docstring">    Log-Like Bernoulli</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; Bernoulli([0,1,1,1,0,0,1,1],0.5)</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line"><tt class="py-docstring">    -5.54517744448</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">    <tt class="py-name">x</tt><tt class="py-op">=</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">    <tt id="link-27" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-27', 'like', 'link-0');">like</a></tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">*</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-number">1.</tt><tt class="py-op">-</tt><tt class="py-name">p</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-28" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-28', 'like', 'link-0');">like</a></tt> </tt>
</div><a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line"> </tt>
<a name="Gamma"></a><div id="Gamma-def"><a name="L174"></a><tt class="py-lineno">174</tt> <a class="py-toggle" href="#" id="Gamma-toggle" onclick="return toggle('Gamma');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.like-module.html#Gamma">Gamma</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt><tt class="py-param">alpha</tt><tt class="py-op">,</tt><tt class="py-param">beta</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Gamma-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Gamma-expanded"><a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line"><tt class="py-docstring">    Log-Like Gamma</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; Gamma([2,3,7,6,4],2,2)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line"><tt class="py-docstring">    -11.015748357</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">    <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">    <tt class="py-name">beta</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">beta</tt><tt class="py-op">)</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">    <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">size</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">    <tt class="py-comment">#Normalizing constant</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line">    <tt id="link-29" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-29', 'like', 'link-0');">like</a></tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-name">n</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">gammaln</tt><tt class="py-op">(</tt><tt class="py-name">alpha</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">alpha</tt><tt class="py-op">*</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">beta</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line">    <tt class="py-comment"># Kernel of the distribution</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">    <tt id="link-30" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-30', 'like', 'link-0');">like</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">alpha</tt> <tt class="py-op">-</tt> <tt class="py-number">1.0</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-name">x</tt><tt class="py-op">/</tt><tt class="py-name">beta</tt><tt class="py-op">)</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-31" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-31', 'like', 'link-0');">like</a></tt> </tt>
</div><a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">     </tt>
<a name="Beta"></a><div id="Beta-def"><a name="L189"></a><tt class="py-lineno">189</tt> <a class="py-toggle" href="#" id="Beta-toggle" onclick="return toggle('Beta');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.like-module.html#Beta">Beta</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt><tt class="py-param">a</tt><tt class="py-op">,</tt><tt class="py-param">b</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Beta-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Beta-expanded"><a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line"><tt class="py-docstring">    Log-Like Beta</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; Beta([.2,.3,.7,.6,.4],2,5)</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line"><tt class="py-docstring">    -0.434845728904</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line">    <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">    <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">size</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line">    <tt class="py-comment">#Normalizing constant</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">    <tt id="link-32" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-32', 'like', 'link-0');">like</a></tt> <tt class="py-op">=</tt> <tt class="py-name">n</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">gammaln</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">+</tt><tt class="py-name">b</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-name">gammaln</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-name">gammaln</tt><tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">    <tt class="py-comment"># Kernel of the distribution</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line">    <tt id="link-33" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-33', 'like', 'link-0');">like</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">-</tt><tt class="py-number">1.0</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">-</tt><tt class="py-number">1.0</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-number">1.0</tt><tt class="py-op">-</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-34" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-34', 'like', 'link-0');">like</a></tt> </tt>
</div><a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line"> </tt>
<a name="Simple"></a><div id="Simple-def"><a name="L203"></a><tt class="py-lineno">203</tt> <a class="py-toggle" href="#" id="Simple-toggle" onclick="return toggle('Simple');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.like-module.html#Simple">Simple</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt><tt class="py-param">w</tt><tt class="py-op">,</tt><tt class="py-param">a</tt><tt class="py-op">,</tt><tt class="py-param">start</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Simple-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Simple-expanded"><a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line"><tt class="py-docstring">    find out what it is.</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">    <tt class="py-name">m</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line">    <tt class="py-name">n</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">    <tt id="link-35" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-35', 'like', 'link-0');">like</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">    <tt class="py-name">s</tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">/</tt><tt class="py-name">w</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">    <tt id="link-36" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-36', 'like', 'link-0');">like</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">+</tt><tt class="py-name">s</tt><tt class="py-op">)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-37" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-37', 'like', 'link-0');">like</a></tt> </tt>
</div><a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">     </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt><tt class="py-op">==</tt><tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">doctest</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line">    <tt class="py-name">doctest</tt><tt class="py-op">.</tt><tt class="py-name">testmod</tt><tt class="py-op">(</tt><tt class="py-name">verbose</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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